The Rocket War
by gallantmon7196
Summary: After his devastating loss against Tobias, Ash goes missing with all of his pokemon and the last person to see him is a Nurse Joy. Three years after his disappearance, Team Rocket launches a world wide campaign to take over all of the regions, killing all who oppose. Gary, May, Brock and the others team up to repel the enemy, but wonder one thing. Where is their missing friend.
1. Chapter 1

**_IMPORTANT!_****Before any of you begin to wonder. No, this is not a betrayal story where all of Ash's friends believe that he should quit being a pokemon trainer. Those are for the most part stupid and extremely cliche at this point. This is something new and entirely different.**

**Also, I don't have any pairings planned with Ash. Just a good friendship.**

**Note: There will be a few OC's in this story. Mostly to serve as side characters and will be based of an actual cannon characters. So for example: children, cousins, parents and so on.**

**Now on with the story.**

* * *

Prologue Part 1

* * *

###Lily in the Valley conference, Semi-final match: Ash vs. Tobias###

"Pikachu, use Volt Tackle!"

The small yellow mouse pokemon flipped around in the air, engulfing himself in a massive amount of electricity. The pokemon's speed of falling increased exponentially, becoming a yellow comet. Pikachu collided with the on coming beam of pink energy, slowly tearing through it. Ash, from his spot in the trainer box, called out to his first pokemon.

"Come on Pikachu, full power!"

The electric type nodded in confirmation and pushed all of his remaining power into this attack. He got closer and closer to the Latios. Allowing them both to be able to see the white of the other's eyes.

"Now use Iron Tail!"

Without a second thought, Pikachu willed his tail to become covered in a substance harder than steel before swinging it with all his might. The leftover electricity from the Volt Tackle only adding to the power. The electrified metal tail sliced through the origin sphere of the Luster Purge, releasing the energy in a stadium shaking explosion. The force sent out by the explosion through everyone into the backs of their seats, and caused them to start coughing from the smoke. The two trainers, Ash Ketchum and Tobias Fabularis, covered their eyes from the smoke, so as to not get blinded. The commentator for the battle spoke to the crowd and the viewers.

_"That last attack and the resulting explosion has managed to make all of our camera equipment out of commission. Some of our in house experts claim that the remaining electricity stored inside pikachu's body was released all at once with the use of Iron Tail. Please wait patiently for the smoke to clear." _

Everyone waited with baited breath. For a full three minutes no one spoke, or even moved. Everyone sat at the edge of their seats, leaning in as close as they could. Ash stood in his designated spot, using all of his will power to keep himself from running out onto the field.

"Come on Pikachu. Please be alright."

Finally, the smoke began to clear. As it thinned out, two lumps, a small one and a larger one, could be seen center field. When smoke fully cleared, Pikachu and Latios both appeared, completely exhausted. The referee raised the red flag he was holding.

"Pikachu and Latios are both unable to battle. This makes Tobias Fabularius the winner."

Almost immediately, the crowd erupted into a deafening cheer. Ash, without any prompting ran out onto the field, while Tobias himself walked out. Ash went over and picked up Pikachu. The electric pokemon didn't have any serious injuries to speak of, he was just tired. Lightly hugging the pokemon, Ash spoke to him softly.

"You did great, Pikachu. We'll win next time."

The pokemon smiled happily, before falling asleep. Ash smiled to himself. He could not have asked for a better friend.

"Ash?"

The young trainer looked up to see Tobias standing in front of him. Latios was levitating to his side.

"Yes?"

Tobias extended his hand forward for Ash to shake.

"I would like to thank you for one of the toughest battles I've had for a long time. You are the first person in years to be able to defeat my Darkrai. I look forward to the next time that we have a chance to battle."

Ash smiled and extended his own hand to shake Tobias'.

"Yeah, I eagerly await our rematch. And next time I won't go as easy on you as I did this time."

The older trainer smiled at the remark of the younger one. Nodding to each other, they both turned and exited the stadium.

* * *

Four figures sat at their seats in the crowd, three humans and a pokemon. All of them had sad and worried expressions on their faces due to their friend's loss. The only girl in the group was the first to speak.

"What's Ash going to do? He came so far, he was so close. Brock, what do you think is going to happen?"

The oldest member of the group turned to his friend, a sad smile on his face.

"Ash'll bounce back soon, he always does. We just need to give him some space to think things out. In a day of two he'll be fine."

The blunette nodded slowly, showing that she understood. Next to her, a boy with wild blonde hair and a orange and white striped shirt decided to join in.

"He'll be okay, Dawn. Or else, I'm going to fine him."

Dawn gave small happy smile at her friend's obsession with fining people. Nodding to Barry and then Brock, all three stood up and Dawn picked up Piplup, her beginner pokemon. The small group of friends exited the stadium with the masses of other people.

* * *

Ash Ketchum walked into the main Pokemon Center used by the participates of the conference. Walking up to the empty counter, he set Pikachu down and waited patiently for the Nurse Joy to arrive. While waiting, he though back to his battle with Tobias and what he should have done differently.

"Stupid. Stupid. Stupid."

He slammed his fist down on the counter at what he felt was extreme stupidity on his part. He thought how he should have had Charizard in his team, and maybe even Infernape, instead of Gible and Torkoal. He was going against a trainer who uses legendary class pokemon, and he went in completely under-prepared. He slammed his fist into the counter again, effectively waking up Pikachu. The electric mouse pokemon slowly opened his eyes and looked at his trainer. Upon seeing the frustration in Ash's eyes, Pikachu came over and patted Ash's arms with his small paws. The young trainer's eyes immediately softened at Pikachu's working attempt to calm him down.

"Hey Pikachu. Sorry I woke you up. Once Nurse Joy gets here, I'll let her take a look at you."

As if on queue, Nurse Joy walked in from the back area. Her hair was messy with strands sticking out everywhere. Putting on a weary smile, she walked over to Ash.

"I'm sorry for the delay, a Rhyperior had woken up after being knocked out and had panicked a little. Now, how may I help you?"

Ash pulled out the five pokeballs attacked to his belt and handed them over to the nurse.

"I would like you to heal my pokemon, please. And Pikachu too."

The Joy smiled brightly and took them.

"I would gladly take them and heal them. It'll just take a few minutes."

Ash nodded, and as soon as she appeared, the Nurse Joy dissapeared into the medical area. Almost immediately, Ash released a breath he didn't know he was holding. He then proceeded to walk over to the phone area. Going to any of the empty ones, he picked the receiver and dialed in the first number. After a few rings, the person picked up on the other end. Smiling as the voice of his mother answered.

"Hey Mom, it's Ash."

"..."

"You saw the match?"

"..."

"Thanks, I'm glad you are happy."

"..."

"Yes I changed my underwear everyday. And yes, I did have a fun time."

"..."

"I'm probably going to come home for a while and have some down time. Think about what to do next."

"..."

"Yeah, he's the next one I'm going to call."

"..."

"I don't know where he is, he never told me."

"..."

"I'll be sure to pass on the message. I have to go, he's expecting me to call."

"..."

"I love you too. Bye."

Ash hung up the phone, feeling as though a small amount of the weight of the world has been lifted off of his shoulders. He felt a small pain in his chest for lying to his mother, but he had too. He had one call down, and still has one more call to make. The tough one. Picking up the receiver again, he dialed another number. He only had to wait after one ring before the other side picked up. Ash smiled at the greeting from the other side.

"Hey man, it's Ash. How are things one your end?"

"..."

"Well of course it's cold. What did you expect, a tropical beach?"

"..."

"My match? I lost, big time."

"..."

"He only had to use two pokemon, a Drakrai and a Latios, to wipe out my entire team."

"..."

"No I had just beaten Paul, the one I've told you about, yestarday. I felt like I was untouchable."

"..."

"I know never to feel that way, you've told me multiple times! Listen, I'll be back in Kanto in a few days and hoping we could see each other, it's been a few years since we've talked face to face. How does that sound?"

"..."

"Good see you in a week man."

"..."

"Alright, I'll bring ketchup. Bye"

Ash hung up the phone with a small smile on his face. The call had gone better than he could have hoped, granted he's going to get an earful about being under prepared in a week, but the call had gone well. Ash suddenly heard the intercom come to life.

_"Ash Ketchum, your pokemon are all healed. Repeat. Ash Ketchum your pokemon are all healed. Please report to the main counter." _

After a moments hesitation, Ash Ketchum walked up to the now brightly smiling Nurse Joy. Once he arrived to the counter, the nurse happily handed a tray to him, showing five pokeballs and a completely revitalized Pikachu.

"Here you go. None of the pokemon were too badly hurt, they were simply tired."

Ash nodded before taking the tray.

"Thank you for healing my pokemon, Nurse Joy."

"You're absolutely welcome. Is there anything else that I can help you with?"

As Pikachu climbed up onto his shoulder, Ash thought for a moment. It didn't take long because almost immediately, something came to mind.

"Yes, actually, I would like to check out of my room."

The nurse nodded as she turned to a computer.

"Okay, if you don't have anything in your room that needs to be retrieved, then I will just need your room key."

Ash dug into his pocket and pulled out a key attached to a metal ring with a plastic tag saying his room number on it. Though the use of a metal key was slightly outdated, all centers had them because they were reliable and trainers were less likely to lose them. Ash proceeded to place the key onto the counter. When the Nurse Joy saw it, she smiled.

"Well then, that should be it. Have a nice day."

Ash nodded as he turned and walked out of the door.

* * *

**So, what do you all think? Good, bad, cliche, not cliche, or just plan ugly. Tell me through reviews.**

**Also, if anyone can guess who Ash was talking to on the second call AND their relation with the young trainer, there will be a special prize. I haven't decided just yet.**

**Until Next Time.**


	2. Prologue Part 2

**Hello and welcome to part two of this story's prologue chapters. I am actually at a cross roads right now. I can't decide whether or not to continue on with the prologue for another two updates or to jump right into the main story. Leave your opinion in a review, or PM me.**

**I would like to thank CaptainPrice for being the first reviewer for this story. I hope that he is the first of many.**

**Now Let's get on with the story!**

**Disclaimer: I, Gallantmon7196, do not in any way, shape, or form own Pokemon. I only own the plot.**

* * *

Prologue Part 2

* * *

###Lily of the Valley Island, Main Port###

"Here you go sir, one ticket for the Bullet Ship from here straight to Vermillion City."

The official in the booth handed Ash the ticket board the ship. Ash Smiled has he took the ticket, and then gave a slight bow in gratitude.

"Thank you for the ticket. When is the Bullet Ship set to leave?"

"Oh, I say in about an hour. Your lucky to get the ticket now, we were almost out."

Ash simply nodded before turning away from the booth and heading towards the ship. He turned his head and started to scratch just behind the ears of his ever faithful companion.

"Well Pikachu, we're heading home. I hope Brock, Dawn, and Barry don't mind if the two of us leave early, it is important."

His ever faithful friend nodded his head in agreement. Ash walked over to the boat and up the boarding ramp. He handed his ticket to the sailor stationed there before making his way onto the rear observation deck. He looked over the water and at the beautiful setting sun. He stood there for a while, watching as the sun got lower and lower in the sky, the circle of light turning from a brilliant yellow to a calming orange. Ash contemplated whether he was doing the right thing, leaving his friends like this without so much as say a good bye. Sighing one last time he stood up from his leaning position and headed back inside toward his room.

* * *

###Lily of the Valley Island, Right outside the main Shopping Area###

Brock and Barry struggled to walk due to the massive amount of shopping bags they were each carrying. Dawn strode ahead of them with Piplup at her side. A small white bag in her left hand and a medium sized vermilion gold bag hanging from the crook of her right elbow. A smile on her face. She put a little jump into her step and hurried forward with Piplup. Once she had gone about fifteen feet, she turned back to two of her friends and yelled back at them.

"Come on guys. It's getting dark!"

Barry managed to shift the bags ever so slightly so that he could look forward and talk to Dawn.

"Yeah well, we would be moving faster if you hadn't gone on a shopping spree at all of the gift shops."

Dawn's face formed into a small pout before she and Piplup slowed down and waited for the boys to catch up. She thought of the battle between Ash and Tobias. She frowned at how unfairly one sided the battle was, even from the beginning. Before she could think any further, Barry and Brock had caught up and proceeded to walk past her. The young coordinator walked up alongside two of her friends.

"So, what do you guys plan on doing after the tournament ends?"

Brock smiled slightly before answering.

"I'm actually going to head back home to Pewter City. I'm going to see how the gym is doing and all of my siblings. What about you, Dawn?"

Dawn smiled brightly over at Brock.

"I'm actually going to travel through the Hoenn region. I'll take in the sights and participate in as many contests as I can. What about you, Barry?"

The blunette looked over to her other friend that she had made since starting her journey. The overly hyper active blonde put on a triumphant smile while his eyes gleamed with determination.

"I'm going all the way to the Unova region and compete for the champion title over there."

Dawn and Brock were perplexed, the name of the region sounded familiar, but they couldn't think of why.

"The Unova region?"

"You know the Unova Region, it's where Castelia City is."

Brock and Dawn looked at the blonde with a mixture of surprise and envy as recognition of the region clicked in their minds. Surprise because of how far away Barry was deciding to go. The region was twenty hour plane ride from the main airport in the Kanto region, and that the region was halfway across the world. The envy came from the fact that Barry was going to Castelia City and they weren't. Everyone knew about Castelia City, or more specifically the Castelia Cone, said to be the most perfect ice cream in the world. It is said to have the perfect consistency and the perfect flavor. Brock's eyebrow twitched slightly while Dawn was completely red with jealously.

"You lucky...LUCKY...Well, you're just lucky!"

Barry through his head back to give a loud, almost mocking, laugh. Dawn continued to fume at him, her face getting redder and redder. As she continued to look at Barry, an idea took hold and a scheming smirk spread across her face. She silently stopped walking, with her two friends being oblivious to her actions. Turning to Piplup, the two of them shared the smirk.

"Piplup, how about we show Barry here our latest contest move that we've been practicing."

The water-type nodded imediately. Taking a deep breath, it waited for it's trainer's command. Dawn nodded too and immediately called to Barry ahead.

"Hey Barry, want to see Piplup's new move?"

The blond teen looked back at them with a bored expression.

"Not now. Can I see it later-"

"Too bad, Piplup, use Ice Beam!"

The small penguin unleashed three tendrils of frozen water at the unfortunate trainer. Barry could only give off a surprised noise before being frozen into a block of ice, shopping bags still in hand. Dawn and Piplup smiled to themselves confidently before continuing to walk. Leaving the frozen Barry with a stunned and slightly nervous Brock. Releasing Happiny, Brock smiled at the baby pokemon. The pink egg shaped pokemon merely jumped up and down in happiness of being out of confinement.

"Happiny, could you help me with carrying Barry to the Pokemon Center to thaw him out?"

Happiny gave it's best impression of a salute before rushing over to the frozen trainer. It effortlessly heaved the ice over it's head with one of it's short stubby arms. Happy with itself, Happiny ran off in the direction of the Pokemon Center. Shaking his head, Brock followed closely behind. During the rest of the walk, the aspiring breeder thought about what he'll do when he get's back to Pewter city. If his mom hasn't tried to convert the gym into something else again, he'll probably substitute for Forrest. To give his brother some time off. His thoughts eventually turned toward one of his oldest friends, Ash. Brock began to worry for the younger trainer, who looked like he was going to be able to at least get to the final match. Ash had worked so hard for the past four years that now it feels as though that had all gone to waist. Before could continue thinking about his friend, he felt a vibrating in his pocket. Reaching his hand in and fishing his cellphone out, he pressed the call button.

"Hello?"

_"Hi Brock, is Ash with you?"_

"No Mrs. Ketchum, he isn't. Is something the matter?"

_"I'm just a little worried for him. I tried to call him earlier, but he wasn't picking up his cellphone and I was wondering if he was just with you and Dawn."_

Mrs. Ketchum's worry could be considered serious. Ash wasn't one to not answer his phone, especially if a call was from his mother.

"I think he went straight to the his hotel room after the match. I'll go check on him, but I think that he is merely sleeping off the match with Pikachu. The two had a rough day"

_"I know, I saw the match. Everyone in the town thought that he was going to win it, somehow able to pull out some miracle and..."_

There was an awkward silence as Delia Ketchum finished what she was saying in a tone to soft for Brock to hear.

"I'll try and talk to him tonight, but if I can't reach him, I'll get him to call you first thing in the morning."

_"Oh Thank you Brock! Ash is really lucky to have a friend like you. Goodnight."_

"Goodnight Mrs. Ketchum, I'll call in he morning if anything comes up."

As he heard the other side of the line hang up, he pressed the button to end the call. By now, Brock was at the entrance of the Pokemon Center that was also the hotel that he, Ash, Dawn and Barry were staying in. It was night right now and all of the nocturnal pokemon were sending out their cries, causing Brock to hurry inside. As he walked up, the automatic doors opened, allowing him access to the interior of the building. Walking him, he nodded to the sleepy Nurse Joy as she dealt with thawing out Barry. Happiny jumped up into his arms as soon as she spotted him. Smiling again, Brock carried Happiny with him to the elevator. Once inside, Brock rocked the small pokemon back and forth before it eventually fell asleep in his hands. Once he reached his floor, he stepped out and walked down the hall. Right before he reached his room, he stopped in front of Ash's. Knocking softly, he waited a moment before speaking.

"Ash, it's Brock. Your mom called me, she worried about you and wants you to call her. I know that this oss was hard for you, but this is so unlike you. You always bounced back. Sure you would get disappointed, but that lasted only a minute and you would be back to your old self. Please Ash, I'm your friend and I want you to know that everyone is proud of you."

Silence was the only response that Brock received. Silently nodding to himself, Brock turned and walked over to his room. Entering it, he wondered how his friend was going to be in the morning.

* * *

###Mt. Silver###

A lone figure stood at the top of a cliff, looking down at everything before him. Today had been one of those rare days when the almost constant cloud cover was gone and the constant snow had subsided. On these days, a person is able to witness one of the most beautiful things this world has to offer, the view from the peak of Mt. Silver. From up there, you feel as though you can see the entire world, and that everything is within reach. The lone figure sighed contently, this is what he came up here for, to feel as though nothing is impossible.

* * *

**So what did you all think? Trust me when I say that everything is pretty much planned out, there aren't any continuity errors. Also, yes I understand that Mt. Silver is cliche but that was actually the only time we'll be at the summit. Ever.**

**So what will you all choose? The Alpha or The Omega?**

**Until Next Time.**


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